Search bioRxiv⌕ Search

bioRxiv · 10.64898/2026.03.23.713701

For MSTd, Autoencoding is all you need

Abstract

While goal-driven artificial neural networks (ANNs) have successfully modeled important aspects of the primate ventral stream, their efficacy for the dorsal stream remains unclear. Here, we investigated how computational objectives and architectural constraints influence the neural alignment to MSTd, a dorsal area that demonstrates selectivity to complex optic flow patterns and is linked to self-motion perception. We systematically evaluated the neural alignment between 54 ANNs and Non-negative Matrix Factorization (NNMF) against key neurophysiological optic flow tuning properties of MSTd. We optimized these models on either a supervised self-motion estimation task (accuracy-optimized) or an unsupervised input reconstruction task (autoencoding) using both raw optic flow and model MT-encoded signals. Interestingly, accuracy on the self-motion task does not predict neural alignment. Instead, model performance bifurcates based on both objective and input encoding: autoencoders utilizing MT-like input signals consistently achieve superior correspondence with MSTd tuning preferences. Explicitly enforcing sparsity or non-negativity does not improve alignment; rather, these constraints often degrade the match to biological data. Furthermore, we demonstrate that neural alignment remains largely unaffected even when the pressure to generate an efficient code with few units is eased, suggesting that dimensionality reduction may not be a primary driver of MSTd-like tuning. Taken together, our results indicate that the tuning properties of MSTd are better explained by an unsupervised reconstruction-based objective than by supervised task optimization, suggesting a fundamental difference in the computational principles that govern the dorsal and ventral streams. Significance StatementGoal-driven neural networks have revolutionized our understanding of the ventral visual stream, yet their effectiveness in modeling the dorsal stream remains less clear. We systematically evaluated 54 neural network models to identify the computational principles that drive neural-like optic flow tuning in dorsal stream area MSTd. Surprisingly, we find that accuracy-optimized models fail to replicate biological tuning. Instead, models that reconstruct motion inputs from a biologically plausible MT-like representation achieve the highest consistency with MSTd neurons. These findings suggest that the organizational principles of dorsal stream area MSTd may be better explained by an unsupervised, reconstruction-based objective rather than one focused on the accuracy of self-motion estimation, suggesting a fundamental difference in the computational objectives of the two visual streams.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Layton, O. W., Steinmetz, S. T.. 2026-03-25. For MSTd, Autoencoding is all you need. https://doi.org/10.64898/2026.03.23.713701

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

The Unreasonable Effectiveness of Cell Types in Describing Neuronal Physiological Features

Single-cell RNA sequencing (scRNA-seq) captures detailed gene expression profiles at scale, while patch-clamp recordings measure intrinsic neuronal electrophysiological properties. Modeling the relations between these two modalities remains a challenge. Here, we compare how well electrophysiological features can be predicted by traditional transcriptomic cell type classification, representations derived from a foundational model (scGPT) pretrained on large-scale scRNA-seq datasets, ion channel-coding genes, and highly variable genes. Using paired transcriptomic and electrophysiological patch-sequencing data from 495 human neurons from neurosurgical tissue, we find that cluster-level cell type representations consistently outperform highly variable gene selection, ion channel gene selection, and context-enriched scGPT embeddings. Notably, performance varies across model architectures and initializations, and the best results are obtained by combining the outputs of separate cell type and scGPT-based models. Together, these findings suggest that traditional discrete cellular classification is highly effective in predicting physiological features. For maximum performance it can be complemented by pretrained transformer models.

neuroscience↗

A nonlinear inhibition pathway underlying cortical responses to tuned holographic optogenetic perturbations

Optogenetics enables causal manipulation of cortical activity. Perturbation responses can be counterintuitive due to network interactions, making theory essential for predicting them. Existing approaches often rely on linear approximations, which fail for many biologically relevant perturbations. Here we develop a nonlinear theory of responses to holographic perturbations in cell-type-specific recurrent networks with structured connectivity. We fit a nonlinear model to mouse V1 data, which shows cotuned-ensemble suppression: perturbing spatially clustered neurons with similar preferred orientations yields markedly stronger short-range suppression than perturbing untuned ensembles. We show that cotuned-ensemble suppression arises from a feature-tuned, nonlinear inhibition pathway implicating somatostatin-positive (SST) interneurons. The theory predicts that cotuned ensembles suppress parvalbumin-positive (PV) neurons but facilitate SST neurons, and links the degree of cotuned-ensemble suppression or facilitation to the variance of the SST response. This framework identifies mechanisms by which nonlinear inhibition sculpts cortical dynamics and establishes a predictive basis for targeted optogenetic interventions.

neuroscience↗

Proteomic signatures of APOE ε4 across human tissues and cell types in Alzheimers disease

The apolipoprotein E {varepsilon}4 (APOE {varepsilon}4) allele is the strongest genetic risk factor for late-onset Alzheimers disease (AD). However, the underlying molecular mechanisms remain unclear. This study included 1691 participants from the Religious Orders Study and Rush Memory and Aging Project (ROSMAP), 1226 participants from the Accelerating Medicines Partnership - Alzheimers Disease (AMP-AD) Diverse Cohorts Study, and 735 participants from the Alzheimers Disease Neuroimaging Initiative (ADNI). To characterise APOE {varepsilon}4 molecular effects, we analysed proteomic data from plasma, cerebrospinal fluid (CSF), and induced pluripotent stem cell (iPSC)-derived astrocytes and neurons, as well as transcriptomic and proteomic data from multiple brain regions. The association of APOE {varepsilon}4 with AD neuropathology was also examined. APOE {varepsilon}4 carriers shared a plasma proteomic signature enriched for immune processes, irrespective of AD diagnosis. A machine learning classifier trained on this signature discriminated APOE {varepsilon}4 carriers from non-carriers in an independent cohort using CSF proteomics. APOE {varepsilon}4 carriage was associated with higher Braak stages and Consortium to Establish a Registry for Alzheimers Disease (CERAD) score. However, only limited APOE {varepsilon}4-associated transcriptomic and proteomic changes were observed in bulk brain tissue, with poor cross-layer concordance. Proteomic analyses of iPSC-derived astrocytes and neurons further revealed cell-type-specific APOE {varepsilon}4-associated changes. APOE {varepsilon}4 is associated with a consistent proteomic signature across plasma and CSF. Its molecular effects in the brain differ across cell types, brain regions and molecular layers. These findings support the need for cell-type-resolved multi-omic studies to elucidate how APOE {varepsilon}4 confers AD risk.

neuroscience↗